Legionella pneumophila

Natural transformation is the mechanism of gene flow controlled by the recipient bacteria. To understand the sources and consequences of variations in transformation rates within species, we experimentally determined them in 786 strains of Legionella pneumophila (Lp) and 496 of Acinetobacter baumannii (Ab). Transformation rates varied by up to six orders of magnitude, with between one third and half of the strains being non-transformable. Most defense systems are associated with lower transformation, except the adaptive CRISPR-Cas systems which show the inverse trend. We find that transformation decreases genetic linkage in both species, thereby providing a recombination-associated benefit. The evolution of transformation was best modelled by large quick changes of the trait (jump processes), resulting in highly variable rates of transformation across the species trees. When enquiring on the reasons of these quick changes, we found an excess of recent transitions towards non-transformability and low persistence of this state, suggesting it is deleterious and thus purged by natural selection. Intragenomic conflicts with chromosomal mobile genetic elements (MGEs) and plasmids could explain these results. Indeed, GWAS revealed systematic negative associations between transformation and MGEs: conjugative elements in Lp, prophages in Ab, and transposable elements in both. In accordance with the existence of such conflicts, transformable strains had fewer MGEs. Even if Ab and Lp have very different lifestyles and genome compositions, they exhibit very similar trends in terms of variation of transformation rates and its determinants, suggesting common causes for the intra-species variability of this mechanism.